2026-03-03 20:57:55,258 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42 --shrink_introns --max_intron_length 1000 2026-03-03 20:58:05,434 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions rna_s1221_S42.fusionreport.tsv --gtf /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42 --shrink_introns --max_intron_length 1000 2026-03-03 20:58:05,434 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/fusion_contigs.ok 2026-03-03 20:58:05,436 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fa 2026-03-03 20:58:05,438 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fa 2026-03-03 20:58:05,438 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/cp_contigs_file_workdir 2026-03-03 20:58:05,440 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf 2026-03-03 20:58:05,443 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf 2026-03-03 20:58:05,443 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/cp_gtf_file_workdir.ok 2026-03-03 20:58:05,444 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf > /tmp/nxf.oLlbwzNzfZ/cytoBand.txt 2026-03-03 20:58:05,509 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf > /tmp/nxf.oLlbwzNzfZ/cytoBand.txt 2026-03-03 20:58:05,509 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/cytoband.ok 2026-03-03 20:58:05,511 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed 2026-03-03 20:58:05,692 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed 2026-03-03 20:58:05,692 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/merged_contig_gtf_to_bed.ok 2026-03-03 20:58:05,694 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed.sorted.bed 2026-03-03 20:58:05,696 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed.sorted.bed 2026-03-03 20:58:05,696 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.bed.bedsort.ok 2026-03-03 20:58:05,698 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed.sorted.bed 2026-03-03 20:58:05,705 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed.sorted.bed 2026-03-03 20:58:05,705 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.bed.bgzip.ok 2026-03-03 20:58:05,707 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed.sorted.bed.gz 2026-03-03 20:58:05,713 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.bed.sorted.bed.gz 2026-03-03 20:58:05,713 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.bed.tabix.ok 2026-03-03 20:58:05,714 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools faidx /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa 2026-03-03 20:58:05,721 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa 2026-03-03 20:58:05,721 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/merged_contig_fai.ok 2026-03-03 20:58:05,723 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf --CPU 16 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.oLlbwzNzfZ/fi_workdir --reads "/tmp/nxf.oLlbwzNzfZ/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42_2.fastp.fastq.gz" 2026-03-03 21:05:19,356 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 7.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fa --max_mate_dist 100000 -G /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf --CPU 16 --out_prefix rna_s1221_S42.star --out_dir /tmp/nxf.oLlbwzNzfZ/fi_workdir --reads "/tmp/nxf.oLlbwzNzfZ/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42_2.fastp.fastq.gz" 2026-03-03 21:05:19,357 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/run_STAR.ok 2026-03-03 21:05:19,358 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam -o /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --remove_dups 2026-03-03 21:05:19,895 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.sortedByCoord.out.bam -o /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --remove_dups 2026-03-03 21:05:19,895 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/mark_dup_reads.ok 2026-03-03 21:05:19,897 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam 2026-03-03 21:05:19,958 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam 2026-03-03 21:05:19,959 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/mark_dups_reads.index.ok 2026-03-03 21:05:19,960 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-03-03 21:05:22,752 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam 2026-03-03 21:05:22,752 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok 2026-03-03 21:05:22,754 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-03-03 21:05:32,420 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam 2026-03-03 21:05:32,420 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok 2026-03-03 21:05:32,422 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary 2026-03-03 21:05:32,441 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary 2026-03-03 21:05:32,441 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/coalesce_junc_n_span.ok 2026-03-03 21:05:32,443 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj 2026-03-03 21:05:32,467 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj 2026-03-03 21:05:32,467 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/init_EM_adj_counts.ok 2026-03-03 21:05:32,469 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-03-03 21:05:32,490 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh 2026-03-03 21:05:32,490 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/filter_by_frag_threshs.ok 2026-03-03 21:05:32,492 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-03-03 21:05:32,508 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs 2026-03-03 21:05:32,508 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_extract_junc_reads.ok 2026-03-03 21:05:32,509 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 16 -bT /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa - | samtools sort -@ 16 - -o /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam" 2026-03-03 21:05:32,554 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 16 -bT /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa - | samtools sort -@ 16 - -o /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam" 2026-03-03 21:05:32,554 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_junc_reads_bam.ok 2026-03-03 21:05:32,556 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam 2026-03-03 21:05:32,561 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam 2026-03-03 21:05:32,561 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/samtools_idx_junc_reads_bam.ok 2026-03-03 21:05:32,563 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed 2026-03-03 21:05:32,592 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed 2026-03-03 21:05:32,592 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.junction_reads.bam.bam_to_bed.ok 2026-03-03 21:05:32,594 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,596 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,596 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.junction_reads.bam.bedsort.ok 2026-03-03 21:05:32,598 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,604 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,604 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.junction_reads.bam.bgzip.ok 2026-03-03 21:05:32,606 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz 2026-03-03 21:05:32,611 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.junction_reads.bam.bed.sorted.bed.gz 2026-03-03 21:05:32,611 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.junction_reads.bam.tabix.ok 2026-03-03 21:05:32,613 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-03-03 21:05:32,628 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs 2026-03-03 21:05:32,628 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/span_reads_acc.ok 2026-03-03 21:05:32,630 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools view -H /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam 2026-03-03 21:05:32,636 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam 2026-03-03 21:05:32,636 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/init_spanning_reads_bam.ok 2026-03-03 21:05:32,637 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 16 -bT /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa - | samtools sort -@ 16 - -o /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam || : 2026-03-03 21:05:32,677 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 16 -bT /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa - | samtools sort -@ 16 - -o /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam || : 2026-03-03 21:05:32,677 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_spanning_reads.ok 2026-03-03 21:05:32,679 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam 2026-03-03 21:05:32,684 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam 2026-03-03 21:05:32,684 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/samtools_index_span_reads_bam.ok 2026-03-03 21:05:32,686 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed 2026-03-03 21:05:32,703 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed 2026-03-03 21:05:32,703 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bam_to_bed.ok 2026-03-03 21:05:32,705 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: sort -k1,1 -k2,2n /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,707 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,707 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bedsort.ok 2026-03-03 21:05:32,708 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: bgzip -f /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,714 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed 2026-03-03 21:05:32,714 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.spanning_reads.bam.bgzip.ok 2026-03-03 21:05:32,715 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: tabix -p bed /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz 2026-03-03 21:05:32,720 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.spanning_reads.bam.bed.sorted.bed.gz 2026-03-03 21:05:32,720 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/rna_s1221_S42.spanning_reads.bam.tabix.ok 2026-03-03 21:05:32,722 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam 2026-03-03 21:05:32,725 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam 2026-03-03 21:05:32,725 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/cp_consol_bam.ok 2026-03-03 21:05:32,726 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: samtools index /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam 2026-03-03 21:05:32,787 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam 2026-03-03 21:05:32,787 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/index_consol_bam.ok 2026-03-03 21:05:32,789 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 2026-03-03 21:05:34,137 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam --max_insert_size 10000000 2026-03-03 21:05:34,137 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_sam_frag_coordss.ok 2026-03-03 21:05:34,138 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.FusionJuncSpan 2026-03-03 21:05:34,179 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.FusionJuncSpan 2026-03-03 21:05:34,179 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_juncspan_fmt.ok 2026-03-03 21:05:34,181 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.Pfam.gff3 2026-03-03 21:05:34,299 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.Pfam.gff3 2026-03-03 21:05:34,299 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_pfam_gff3.ok 2026-03-03 21:05:34,300 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.Pfam.bed 2026-03-03 21:05:34,376 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.Pfam.gff3 > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.Pfam.bed 2026-03-03 21:05:34,376 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_pfam_bed.ok 2026-03-03 21:05:34,378 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.seqsimilar.gff3 2026-03-03 21:05:34,420 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.seqsimilar.gff3 2026-03-03 21:05:34,420 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_seqsim_gff3.ok 2026-03-03 21:05:34,422 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.seqsimilar.bed 2026-03-03 21:05:34,447 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.seqsimilar.gff3 > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.igv.seqsimilar.bed 2026-03-03 21:05:34,447 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/prep_igv_seqsim_bed.ok 2026-03-03 21:05:34,449 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-03-03 21:05:34,499 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa > /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo 2026-03-03 21:05:34,499 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/add_splice_info.ok 2026-03-03 21:05:34,500 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-03-03 21:05:34,682 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.oLlbwzNzfZ/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 2026-03-03 21:05:34,682 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/blast_filter.ok 2026-03-03 21:05:34,683 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir 2026-03-03 21:05:34,705 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir 2026-03-03 21:05:34,705 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/annot_filter.ok 2026-03-03 21:05:34,706 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-03-03 21:05:34,724 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj 2026-03-03 21:05:34,724 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/EM_adj_counts.ok 2026-03-03 21:05:34,726 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-03-03 21:05:48,698 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.23 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM 2026-03-03 21:05:48,698 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/add_FFPM.ok 2026-03-03 21:05:48,700 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa --gtf /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf > /tmp/nxf.oLlbwzNzfZ/fi_workdir/microH.dat 2026-03-03 21:05:48,865 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fa --gtf /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.gtf > /tmp/nxf.oLlbwzNzfZ/fi_workdir/microH.dat 2026-03-03 21:05:48,865 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/microH.dat.ok 2026-03-03 21:05:48,866 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.oLlbwzNzfZ/fi_workdir/microH.dat /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-03-03 21:05:48,890 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.oLlbwzNzfZ/fi_workdir/microH.dat /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH 2026-03-03 21:05:48,890 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/append_microH_info.ok 2026-03-03 21:05:48,892 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: cp /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.tsv 2026-03-03 21:05:48,894 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.tsv 2026-03-03 21:05:48,894 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/cp_final.ok 2026-03-03 21:05:48,896 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv 2026-03-03 21:05:48,911 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv 2026-03-03 21:05:48,912 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/final.abridged.ok 2026-03-03 21:05:48,913 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.oLlbwzNzfZ --json_outfile /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42 2026-03-03 21:05:48,936 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.oLlbwzNzfZ --json_outfile /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fusion_inspector_web.json --file_prefix rna_s1221_S42 2026-03-03 21:05:48,936 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/create_fi_igvjs.ok 2026-03-03 21:05:48,938 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fusion_inspector_web.html 2026-03-03 21:05:49,525 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fusion_inspector_web.json --input_file_prefix rna_s1221_S42 --html_output /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.fusion_inspector_web.html 2026-03-03 21:05:49,526 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/fusion_reports_html.ok 2026-03-03 21:05:49,527 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 2026-03-03 21:05:49,551 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated 2026-03-03 21:05:49,551 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/fusion_annotator.ok 2026-03-03 21:05:49,553 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-03-03 21:05:49,698 INFO Pipeliner.Pipeliner.run at 136 : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.oLlbwzNzfZ/ctat_genome_lib_build_dir > /tmp/nxf.oLlbwzNzfZ/rna_s1221_S42.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 2026-03-03 21:05:49,698 INFO Pipeliner.Pipeliner.run_cmd at 21 : Running: touch /tmp/nxf.oLlbwzNzfZ/chckpts_dir/fusion_coding_region_effect.ok